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. 2016 Jun 17;16:301.
doi: 10.1186/s12879-016-1605-0.

Human Metapneumovirus Epidemiological and Evolutionary Patterns in Coastal Kenya, 2007-11

Free PMC article

Human Metapneumovirus Epidemiological and Evolutionary Patterns in Coastal Kenya, 2007-11

Betty E Owor et al. BMC Infect Dis. .
Free PMC article


Background: Human metapneumovirus (HMPV) is an important global cause of severe acute respiratory infections in young children and the elderly. The epidemiology of HMPV in sub-Saharan Africa is poorly described and factors that allow its recurrent epidemics in communities not understood.

Methods: We undertook paediatric inpatient surveillance for HMPV in Kilifi County Hospital (KCH) of Coastal Kenya between 2007 and 2011. Nasopharyngeal samples collected from children aged 1 day-59 months admitted with severe or very severe pneumonia, were tested for HMPV using real-time polymerase chain reaction (RT-PCR). Partial nucleotide sequences of the attachment (G) and fusion (F) surface proteins of positive samples were determined and phylogenetically analyzed.

Results: HMPV was detected in 4.8 % (160/3320) of children [73.8 % (118/160) of these less than one year of age], ranging between 2.9 and 8.8 % each year over the 5 years of study. HMPV infections were seasonal in occurrence, with cases predominant in the months of November through April. These months frequently coincided with low rainfall, high temperature and low relative humidity in the location. Phylogenetic analysis of partial F and G sequences revealed three subgroups of HMPV, A2 (74 %, 91/123), B1 (3.2 %, 4/123) and B2 (22.8 %, 28/123) in circulation, with subgroup A2 predominant in majority of the epidemic seasons. Comparison of G sequences (local and global) provided a greater phylogenetic resolution over comparison of F sequences and indicated presence of probable multiple G antigenic variants within the subgroups due to differences in amino acid sequence, encoded protein length and glycosylation patterns.

Conclusion: The present study reveals HMPV is an important seasonal contributor to respiratory disease hospitalization in coastal Kenya, with an evolutionary pattern closely relating to that of respiratory syncytial virus.

Keywords: Genetic diversity; Human metapneumovirus; Kenya; Kilifi; Respiratory virus.


Fig. 1
Fig. 1
a Temporal distribution of HMPV positive samples in Kilifi over five years, showing number of positive samples each month on the primary axis and number of samples tested monthly on the secondary axis. Different colours indicate the different epidemics the samples were assigned; b Monthly weather patterns in Kilifi, Kenya in the period 2007–2011
Fig. 2
Fig. 2
Phylogenetic relatedness and temporal divergence of the combined Kilifi and contemporaneous global F protein sequences over the 345-nucleotide portion analyzed. Taxa of Kilifi viruses are coloured red. Node bars indicate the 95 % HPD height interval of the nodes; the node makers size are scaled by posterior support, for Kilifi, coastal Kenya 2007–11
Fig. 3
Fig. 3
Phylogenetic and temporal placement of Kilifi group A G protein sequenced viruses, for Kilifi, coastal Kenya 2007–2011. Panel a A total of 209 viruses compared in G sequences G (53 from Kilifi and 156 collated from GenBank from 7 countries). Branches leading to Kilifi viruses are coloured red. Three letter codes of countries comprising branches without Kilifi representative sequences are indicated next to the vertical line. Panel b 121 viruses that fell within the ancestral node leading to Kilifi viruses were reanalyzed in BEAST. Again branches and leaves of Kilifi viruses are colored red on the phylogenetic temporally calibrated tree. Node bars indicate the 95 % HPD height interval of the nodes; the node maker sizes are scaled by posterior support. The number 1, 2, 3 and 4 represent the three major and one minor cluster of sequences from Kilifi
Fig. 4
Fig. 4
Pie charts showing the genotype distribution by year derived from F sequence analysis of samples from Kilifi, Coastal Kenya 2007-11. Panel a This is based on the 290 F sequences collated from GenBank. Panel b This is based on 123 F sequences generated from samples that were collected in this study at the KCH between 2007 and 2011. The numbers inside the pies indicate the genotype proportions per the respective year

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